Back to Multiple platform build/check report for BioC 3.20: simplified long 

This page was generated on 20240611 15:43 0400 (Tue, 11 Jun 2024).
Hostname  OS  Arch (*)  R version  Installed pkgs 

nebbiolo2  Linux (Ubuntu 22.04.3 LTS)  x86_64  4.4.0 RC (20240416 r86468)  "Puppy Cup"  4679 
palomino4  Windows Server 2022 Datacenter  x64  4.4.0 RC (20240416 r86468 ucrt)  "Puppy Cup"  4414 
merida1  macOS 12.7.4 Monterey  x86_64  4.4.0 Patched (20240424 r86482)  "Puppy Cup"  4441 
kjohnson1  macOS 13.6.6 Ventura  arm64  4.4.0 Patched (20240424 r86482)  "Puppy Cup"  4394 
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname p', except on Windows and Mac OS X 
Package 992/2239  Hostname  OS / Arch  INSTALL  BUILD  CHECK  BUILD BIN  
IgGeneUsage 1.19.0 (landing page) Simo Kitanovski
 nebbiolo2  Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  OK  OK  
palomino4  Windows Server 2022 Datacenter / x64  OK  OK  OK  OK  
merida1  macOS 12.7.4 Monterey / x86_64  OK  OK  OK  OK  
kjohnson1  macOS 13.6.6 Ventura / arm64  OK  OK  OK  OK  
To the developers/maintainers of the IgGeneUsage package:  Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IgGeneUsage.git to reflect on this report. See Troubleshooting Build Report for more information.  Use the following Renviron settings to reproduce errors and warnings.  If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. 
Package: IgGeneUsage 
Version: 1.19.0 
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check install=check:IgGeneUsage.installout.txt library=/Library/Frameworks/R.framework/Resources/library novignettes timings IgGeneUsage_1.19.0.tar.gz 
StartedAt: 20240610 22:38:12 0400 (Mon, 10 Jun 2024) 
EndedAt: 20240610 22:48:42 0400 (Mon, 10 Jun 2024) 
EllapsedTime: 629.8 seconds 
RetCode: 0 
Status: OK 
CheckDir: IgGeneUsage.Rcheck 
Warnings: 0 
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check install=check:IgGeneUsage.installout.txt library=/Library/Frameworks/R.framework/Resources/library novignettes timings IgGeneUsage_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs3.20bioc/meat/IgGeneUsage.Rcheck’ * using R version 4.4.0 Patched (20240424 r86482) * using platform: aarch64appledarwin20 * R was compiled by Apple clang version 14.0.0 (clang1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF8 * using option ‘novignettes’ * checking for file ‘IgGeneUsage/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘IgGeneUsage’ version ‘1.19.0’ * package encoding: UTF8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘IgGeneUsage’ can be installed ... OK * used C++ compiler: ‘Apple clang version 15.0.0 (clang1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... OK Not all R platforms support C++17 * checking installed package size ... NOTE installed size is 6.1Mb subdirectories of 1Mb or more: libs 5.4Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION metainformation ... NOTE License stub is invalid DCF. * checking toplevel files ... OK * checking for leftover files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for nonASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE get_manu : get_manu_run: no visible global function definition for ‘wilcox.test’ get_manu: no visible global function definition for ‘p.adjust’ get_ttest : get_ttest_run: no visible global function definition for ‘t.test’ get_ttest: no visible global function definition for ‘p.adjust’ get_usage : check_paired: no visible global function definition for ‘aggregate’ get_usage: no visible binding for global variable ‘sample_id’ get_usage: no visible binding for global variable ‘gene_name’ get_usage: no visible global function definition for ‘aggregate’ Undefined global functions or variables: aggregate gene_name p.adjust sample_id t.test wilcox.test Consider adding importFrom("stats", "aggregate", "p.adjust", "t.test", "wilcox.test") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd crossreferences ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for nonASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed LOO 344.167 4.122 349.060 DGU 41.057 1.178 42.403 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking rebuilding of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 6 NOTEs See ‘/Users/biocbuild/bbs3.20bioc/meat/IgGeneUsage.Rcheck/00check.log’ for details.
IgGeneUsage.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL IgGeneUsage ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library’ * installing *source* package ‘IgGeneUsage’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang1500.0.40.1)’ using C++17 using SDK: ‘MacOSX11.3.sdk’ clang++ arch arm64 std=gnu++17 I"/Library/Frameworks/R.framework/Resources/include" DNDEBUG I"../inst/include" I"/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/src" DBOOST_DISABLE_ASSERTS DEIGEN_NO_DEBUG DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error DUSE_STANC3 D_HAS_AUTO_PTR_ETC=0 I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/Rcpp/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppParallel/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include' I/opt/R/arm64/include I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppParallel/include' D_REENTRANT DSTAN_THREADS fPIC falignfunctions=64 Wall g O2 c RcppExports.cpp o RcppExports.o In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [Wunusedbutsetvariable] Index count = 0; ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [Wunusedbutsetvariable] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [Wunusedbutsetvariable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [Wunusedbutsetvariable] Index replacements = 0; ^ In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [Wunusedbutsetvariable] int count = 0; ^ 5 warnings generated. clang++ arch arm64 std=gnu++17 I"/Library/Frameworks/R.framework/Resources/include" DNDEBUG I"../inst/include" I"/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/src" DBOOST_DISABLE_ASSERTS DEIGEN_NO_DEBUG DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error DUSE_STANC3 D_HAS_AUTO_PTR_ETC=0 I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/Rcpp/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppParallel/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include' I/opt/R/arm64/include I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppParallel/include' D_REENTRANT DSTAN_THREADS fPIC falignfunctions=64 Wall g O2 c stanExports_dgu.cc o stanExports_dgu.o In file included from stanExports_dgu.cc:5: In file included from ./stanExports_dgu.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [Wunusedbutsetvariable] Index count = 0; ^ In file included from stanExports_dgu.cc:5: In file included from ./stanExports_dgu.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [Wunusedbutsetvariable] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [Wunusedbutsetvariable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^ In file included from stanExports_dgu.cc:5: In file included from ./stanExports_dgu.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [Woverloadedvirtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_dgu.cc:5: In file included from ./stanExports_dgu.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [Woverloadedvirtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_dgu.cc:5: In file included from ./stanExports_dgu.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [Wunusedbutsetvariable] Index replacements = 0; ^ In file included from stanExports_dgu.cc:5: In file included from ./stanExports_dgu.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [Wunusedbutsetvariable] int count = 0; ^ In file included from stanExports_dgu.cc:5: In file included from ./stanExports_dgu.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [Wmismatchedtags] struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> { ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? class ops_partials_edge; ^~~~~ struct In file included from stanExports_dgu.cc:5: In file included from ./stanExports_dgu.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [Wunusedbutsetvariable] int ret = stan::services::error_codes::CONFIG; ^ In file included from stanExports_dgu.cc:5: ./stanExports_dgu.h:925:11: warning: variable 'pos__' set but not used [Wunusedbutsetvariable] int pos__ = std::numeric_limits<int>::min(); ^ In file included from stanExports_dgu.cc:5: In file included from ./stanExports_dgu.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [Wunusedvariable] const T x_extrema = 1 / (1 + a); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder<double>::temme_root_finder' requested here temme_root_finder<T>(lu, alpha), x, lower, upper, policies::digits<T, Policy>() / 2); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here rx = detail::ibeta_inv_imp( ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here return ibeta_inv(a, b, p, static_cast<result_type*>(nullptr), pol); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); ^ 11 warnings generated. clang++ arch arm64 std=gnu++17 I"/Library/Frameworks/R.framework/Resources/include" DNDEBUG I"../inst/include" I"/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/src" DBOOST_DISABLE_ASSERTS DEIGEN_NO_DEBUG DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error DUSE_STANC3 D_HAS_AUTO_PTR_ETC=0 I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/Rcpp/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppParallel/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include' I/opt/R/arm64/include I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppParallel/include' D_REENTRANT DSTAN_THREADS fPIC falignfunctions=64 Wall g O2 c stanExports_dgu_paired.cc o stanExports_dgu_paired.o In file included from stanExports_dgu_paired.cc:5: In file included from ./stanExports_dgu_paired.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [Wunusedbutsetvariable] Index count = 0; ^ In file included from stanExports_dgu_paired.cc:5: In file included from ./stanExports_dgu_paired.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [Wunusedbutsetvariable] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [Wunusedbutsetvariable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^ In file included from stanExports_dgu_paired.cc:5: In file included from ./stanExports_dgu_paired.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [Woverloadedvirtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_dgu_paired.cc:5: In file included from ./stanExports_dgu_paired.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [Woverloadedvirtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_dgu_paired.cc:5: In file included from ./stanExports_dgu_paired.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [Wunusedbutsetvariable] Index replacements = 0; ^ In file included from stanExports_dgu_paired.cc:5: In file included from ./stanExports_dgu_paired.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [Wunusedbutsetvariable] int count = 0; ^ In file included from stanExports_dgu_paired.cc:5: In file included from ./stanExports_dgu_paired.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [Wmismatchedtags] struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> { ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? class ops_partials_edge; ^~~~~ struct In file included from stanExports_dgu_paired.cc:5: In file included from ./stanExports_dgu_paired.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [Wunusedbutsetvariable] int ret = stan::services::error_codes::CONFIG; ^ In file included from stanExports_dgu_paired.cc:5: ./stanExports_dgu_paired.h:975:11: warning: variable 'pos__' set but not used [Wunusedbutsetvariable] int pos__ = std::numeric_limits<int>::min(); ^ In file included from stanExports_dgu_paired.cc:5: In file included from ./stanExports_dgu_paired.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [Wunusedvariable] const T x_extrema = 1 / (1 + a); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder<double>::temme_root_finder' requested here temme_root_finder<T>(lu, alpha), x, lower, upper, policies::digits<T, Policy>() / 2); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here rx = detail::ibeta_inv_imp( ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here return ibeta_inv(a, b, p, static_cast<result_type*>(nullptr), pol); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); ^ 11 warnings generated. clang++ arch arm64 std=gnu++17 I"/Library/Frameworks/R.framework/Resources/include" DNDEBUG I"../inst/include" I"/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/src" DBOOST_DISABLE_ASSERTS DEIGEN_NO_DEBUG DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error DUSE_STANC3 D_HAS_AUTO_PTR_ETC=0 I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/Rcpp/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppParallel/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include' I/opt/R/arm64/include I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppParallel/include' D_REENTRANT DSTAN_THREADS fPIC falignfunctions=64 Wall g O2 c stanExports_dgu_paired_rep.cc o stanExports_dgu_paired_rep.o In file included from stanExports_dgu_paired_rep.cc:5: In file included from ./stanExports_dgu_paired_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [Wunusedbutsetvariable] Index count = 0; ^ In file included from stanExports_dgu_paired_rep.cc:5: In file included from ./stanExports_dgu_paired_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [Wunusedbutsetvariable] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [Wunusedbutsetvariable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^ In file included from stanExports_dgu_paired_rep.cc:5: In file included from ./stanExports_dgu_paired_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [Woverloadedvirtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_dgu_paired_rep.cc:5: In file included from ./stanExports_dgu_paired_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [Woverloadedvirtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_dgu_paired_rep.cc:5: In file included from ./stanExports_dgu_paired_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [Wunusedbutsetvariable] Index replacements = 0; ^ In file included from stanExports_dgu_paired_rep.cc:5: In file included from ./stanExports_dgu_paired_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [Wunusedbutsetvariable] int count = 0; ^ In file included from stanExports_dgu_paired_rep.cc:5: In file included from ./stanExports_dgu_paired_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [Wmismatchedtags] struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> { ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? class ops_partials_edge; ^~~~~ struct In file included from stanExports_dgu_paired_rep.cc:5: In file included from ./stanExports_dgu_paired_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [Wunusedbutsetvariable] int ret = stan::services::error_codes::CONFIG; ^ In file included from stanExports_dgu_paired_rep.cc:5: ./stanExports_dgu_paired_rep.h:1062:11: warning: variable 'pos__' set but not used [Wunusedbutsetvariable] int pos__ = std::numeric_limits<int>::min(); ^ In file included from stanExports_dgu_paired_rep.cc:5: In file included from ./stanExports_dgu_paired_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [Wunusedvariable] const T x_extrema = 1 / (1 + a); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder<double>::temme_root_finder' requested here temme_root_finder<T>(lu, alpha), x, lower, upper, policies::digits<T, Policy>() / 2); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here rx = detail::ibeta_inv_imp( ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here return ibeta_inv(a, b, p, static_cast<result_type*>(nullptr), pol); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); ^ 11 warnings generated. clang++ arch arm64 std=gnu++17 I"/Library/Frameworks/R.framework/Resources/include" DNDEBUG I"../inst/include" I"/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/src" DBOOST_DISABLE_ASSERTS DEIGEN_NO_DEBUG DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error DUSE_STANC3 D_HAS_AUTO_PTR_ETC=0 I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/Rcpp/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppParallel/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include' I/opt/R/arm64/include I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppParallel/include' D_REENTRANT DSTAN_THREADS fPIC falignfunctions=64 Wall g O2 c stanExports_dgu_rep.cc o stanExports_dgu_rep.o In file included from stanExports_dgu_rep.cc:5: In file included from ./stanExports_dgu_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [Wunusedbutsetvariable] Index count = 0; ^ In file included from stanExports_dgu_rep.cc:5: In file included from ./stanExports_dgu_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [Wunusedbutsetvariable] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [Wunusedbutsetvariable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^ In file included from stanExports_dgu_rep.cc:5: In file included from ./stanExports_dgu_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [Woverloadedvirtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_dgu_rep.cc:5: In file included from ./stanExports_dgu_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [Woverloadedvirtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_dgu_rep.cc:5: In file included from ./stanExports_dgu_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [Wunusedbutsetvariable] Index replacements = 0; ^ In file included from stanExports_dgu_rep.cc:5: In file included from ./stanExports_dgu_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [Wunusedbutsetvariable] int count = 0; ^ In file included from stanExports_dgu_rep.cc:5: In file included from ./stanExports_dgu_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [Wmismatchedtags] struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> { ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? class ops_partials_edge; ^~~~~ struct In file included from stanExports_dgu_rep.cc:5: In file included from ./stanExports_dgu_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [Wunusedbutsetvariable] int ret = stan::services::error_codes::CONFIG; ^ In file included from stanExports_dgu_rep.cc:5: ./stanExports_dgu_rep.h:1055:11: warning: variable 'pos__' set but not used [Wunusedbutsetvariable] int pos__ = std::numeric_limits<int>::min(); ^ In file included from stanExports_dgu_rep.cc:5: In file included from ./stanExports_dgu_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [Wunusedvariable] const T x_extrema = 1 / (1 + a); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder<double>::temme_root_finder' requested here temme_root_finder<T>(lu, alpha), x, lower, upper, policies::digits<T, Policy>() / 2); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here rx = detail::ibeta_inv_imp( ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here return ibeta_inv(a, b, p, static_cast<result_type*>(nullptr), pol); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); ^ 11 warnings generated. clang++ arch arm64 std=gnu++17 I"/Library/Frameworks/R.framework/Resources/include" DNDEBUG I"../inst/include" I"/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/src" DBOOST_DISABLE_ASSERTS DEIGEN_NO_DEBUG DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error DUSE_STANC3 D_HAS_AUTO_PTR_ETC=0 I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/Rcpp/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppParallel/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include' I/opt/R/arm64/include I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppParallel/include' D_REENTRANT DSTAN_THREADS fPIC falignfunctions=64 Wall g O2 c stanExports_gu.cc o stanExports_gu.o In file included from stanExports_gu.cc:5: In file included from ./stanExports_gu.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [Wunusedbutsetvariable] Index count = 0; ^ In file included from stanExports_gu.cc:5: In file included from ./stanExports_gu.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [Wunusedbutsetvariable] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [Wunusedbutsetvariable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^ In file included from stanExports_gu.cc:5: In file included from ./stanExports_gu.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [Woverloadedvirtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_gu.cc:5: In file included from ./stanExports_gu.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [Woverloadedvirtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_gu.cc:5: In file included from ./stanExports_gu.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [Wunusedbutsetvariable] Index replacements = 0; ^ In file included from stanExports_gu.cc:5: In file included from ./stanExports_gu.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [Wunusedbutsetvariable] int count = 0; ^ In file included from stanExports_gu.cc:5: In file included from ./stanExports_gu.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [Wmismatchedtags] struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> { ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? class ops_partials_edge; ^~~~~ struct In file included from stanExports_gu.cc:5: In file included from ./stanExports_gu.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [Wunusedbutsetvariable] int ret = stan::services::error_codes::CONFIG; ^ In file included from stanExports_gu.cc:5: ./stanExports_gu.h:670:11: warning: variable 'pos__' set but not used [Wunusedbutsetvariable] int pos__ = std::numeric_limits<int>::min(); ^ In file included from stanExports_gu.cc:5: In file included from ./stanExports_gu.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [Wunusedvariable] const T x_extrema = 1 / (1 + a); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder<double>::temme_root_finder' requested here temme_root_finder<T>(lu, alpha), x, lower, upper, policies::digits<T, Policy>() / 2); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here rx = detail::ibeta_inv_imp( ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here return ibeta_inv(a, b, p, static_cast<result_type*>(nullptr), pol); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); ^ 11 warnings generated. clang++ arch arm64 std=gnu++17 I"/Library/Frameworks/R.framework/Resources/include" DNDEBUG I"../inst/include" I"/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/src" DBOOST_DISABLE_ASSERTS DEIGEN_NO_DEBUG DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error DUSE_STANC3 D_HAS_AUTO_PTR_ETC=0 I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/Rcpp/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppParallel/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include' I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include' I/opt/R/arm64/include I'/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppParallel/include' D_REENTRANT DSTAN_THREADS fPIC falignfunctions=64 Wall g O2 c stanExports_gu_rep.cc o stanExports_gu_rep.o In file included from stanExports_gu_rep.cc:5: In file included from ./stanExports_gu_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [Wunusedbutsetvariable] Index count = 0; ^ In file included from stanExports_gu_rep.cc:5: In file included from ./stanExports_gu_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [Wunusedbutsetvariable] Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [Wunusedbutsetvariable] Index nsuper_et = 0; // Number of relaxed snodes in the original etree ^ In file included from stanExports_gu_rep.cc:5: In file included from ./stanExports_gu_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [Woverloadedvirtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_gu_rep.cc:5: In file included from ./stanExports_gu_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [Woverloadedvirtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_gu_rep.cc:5: In file included from ./stanExports_gu_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [Wunusedbutsetvariable] Index replacements = 0; ^ In file included from stanExports_gu_rep.cc:5: In file included from ./stanExports_gu_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigen.h:25: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [Wunusedbutsetvariable] int count = 0; ^ In file included from stanExports_gu_rep.cc:5: In file included from ./stanExports_gu_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [Wmismatchedtags] struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> { ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? class ops_partials_edge; ^~~~~ struct In file included from stanExports_gu_rep.cc:5: In file included from ./stanExports_gu_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [Wunusedbutsetvariable] int ret = stan::services::error_codes::CONFIG; ^ In file included from stanExports_gu_rep.cc:5: ./stanExports_gu_rep.h:802:11: warning: variable 'pos__' set but not used [Wunusedbutsetvariable] int pos__ = std::numeric_limits<int>::min(); ^ In file included from stanExports_gu_rep.cc:5: In file included from ./stanExports_gu_rep.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721: /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [Wunusedvariable] const T x_extrema = 1 / (1 + a); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder<double>::temme_root_finder' requested here temme_root_finder<T>(lu, alpha), x, lower, upper, policies::digits<T, Policy>() / 2); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here rx = detail::ibeta_inv_imp( ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here return ibeta_inv(a, b, p, static_cast<result_type*>(nullptr), pol); ^ /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<>>>' requested here return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); ^ 11 warnings generated. clang++ arch arm64 std=gnu++17 dynamiclib Wl,headerpad_max_install_names undefined dynamic_lookup L/Library/Frameworks/R.framework/Resources/lib L/opt/R/arm64/lib o IgGeneUsage.so RcppExports.o stanExports_dgu.o stanExports_dgu_paired.o stanExports_dgu_paired_rep.o stanExports_dgu_rep.o stanExports_gu.o stanExports_gu_rep.o L/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppParallel/lib/ Wl,rpath,/Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/RcppParallel/lib/ ltbb ltbbmalloc F/Library/Frameworks/R.framework/.. framework R Wl,framework Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4arm64/Resources/library/00LOCKIgGeneUsage/00new/IgGeneUsage/libs ** R ** data ** inst ** bytecompile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (IgGeneUsage)
IgGeneUsage.Rcheck/tests/testthat.Rout
R version 4.4.0 Patched (20240424 r86482)  "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64appledarwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for online help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(IgGeneUsage) > > test_check("IgGeneUsage") Tests stan model [ FAIL 0  WARN 0  SKIP 0  PASS 4 ] > > proc.time() user system elapsed 10.459 0.490 10.554
IgGeneUsage.Rcheck/IgGeneUsageEx.timings
name  user  system  elapsed  
DGU  41.057  1.178  42.403  
IGHV_Epitopes  0.003  0.001  0.004  
IGHV_HCV  0.004  0.002  0.006  
Ig  0.003  0.001  0.003  
Ig_SE  0.030  0.002  0.032  
LOO  344.167  4.122  349.060  
d_zibb_1  0.002  0.001  0.003  
d_zibb_2  0.002  0.001  0.003  
d_zibb_3  0.002  0.001  0.002  
d_zibb_4  0.003  0.001  0.003  
d_zibb_5  0.002  0.001  0.003  
d_zibb_6  0.003  0.001  0.005  